rs12447486

chr16-3072281-G-Achr16-3072281-G-Cchr16-3072281-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000525377.6(IL32):c.339+4042G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 147,240 control chromosomes in the GnomAD database, including 19,744 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (19744 hom., cov: 29)
• Consequence: IL32 ENST00000525377.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232

Genes affected

IL32 (HGNC:16830): (interleukin 32) This gene encodes a member of the cytokine family. The protein contains a tyrosine sulfation site, 3 potential N-myristoylation sites, multiple putative phosphorylation sites, and an RGD cell-attachment sequence. Expression of this protein is increased after the activation of T-cells by mitogens or the activation of NK cells by IL-2. This protein induces the production of TNFalpha from macrophage cells. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL32	ENST00000525377.6	c.339+4042G>A		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.508 AC: 74733 AN: 147128 Hom.: 19740 Cov.: 29

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.521

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.508 AC: 74769 AN: 147240 Hom.: 19744 Cov.: 29 AF XY: 0.508 AC XY: 36542 AN XY: 71912

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.522

Alfa AF: 0.415 Hom.: 967

Asia WGS AF: 0.465 AC: 1620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.8
Dann	Benign	0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12447486; hg19: chr16-3122282; COSMIC: COSV50405602;